Good afternoon to everyone,
I’m trying to run a differential abundance analysis on my 16S dataset, and, as I explained in this topic and @Nicholas_Bokulich suggested me, I’m trying to use songbird by @mortonjt rather than gneiss, since a plugin I need, apparently, is deprecated.
I’m sticking to the installation and run procedure suggested in the GitHub guide and decided to use songbird through QIIME2 rather than as standalone tool.
Apparently, I can start from .qza artifacts directly, and I picked the FeatureTable[Frequency] obtained by
qiime dada2 denoise-paired and filtered from mitochondrial and chloroplastic sequences through
qiime taxa filter-table.
I ran the following:
qiime songbird multinomial --i-table table-no-clo-mit.qza --m-metadata-file songbird/16S_metadata_songbird.tsv --p-formula "Site+Soil" --p-epochs 10000 --p-differential-prior 0.5 --p-summary-interval 1 --o-differentials songbird/differentials.qza --o-regression-stats songbird/regression-stats.qza --o-regression-biplot songbird/regression-biplot.qza --verbose
I got this error:
Plugin error from songbird:
Column length mismatch: 15 vs. 0
See above for debug info.
I’m attaching the whole log here.
I get the same error if I use the standalone version, omit optional parameters of the
qiime songbird multinomial plugin and the column length error changes (17 vs. 0) if I use the unfiltered table.
I’m also attaching my metadata and my FeatureTable files (this is a temporary link).
I’m running QIIME2-2019.7
Any idea what could be wrong?
Thanks in advance for your help!